This situation is nearly the exact as mine. I am struggling with the same difficulties with the communication in my long distance relationship. Those kind of misunderstandings between my boyfriend and I happen all of the time. Have you spoken with him about this? Explained your difficulties understanding the clues?
Also, tell him to try and be more direct with you. If something bothers or upsets him, ask him to clarify if that was your intention, or tell you that what you said was upsetting AND WHY.
If you are blunt or being literal, and there is no underlying negative emotion or extra meaning tied to your words, then many people will try to put their own meaning in there. They see the "blank space" where they think should be some sort of extra or double meaning, and they fill it in with whatever they first think of.
It's like giving a black and white painting to a small child, and they immediately think that they should color it in, because in their mind it's not a real piece of art until it is colorful. The colored in painting looks messy and childish. Any judgment about the painting cannot be done without seeing the colorful mess.
The black and white painting would be a literal or blunt statement. It is what it is, you're not trying to say anything else. Or maybe you are, but it isn't anything negative. The child would be your bf or anyone who misinterprets what you say, and by trying to fill in their own meaning (coloring the white in the black and white painting), they often make a mess of the situation by creating problems where there originally were none. Maybe he WANTS the conflict. Some people are like that, or they simply have hidden or suppressed feelings that they do not know how to express, so they search for any outlet where they can vent their anger or sadness. I do not know your bf or you or any of your specific conversations so I cannot say what he is misreading or why.
This is really something you are going to have to resolve with him, because it is not as simple a matter as a solution to a broken appliance. Communication is subjective in most cases, unfortunately. If he cannot understand you, then perhaps you should study relationship communication (there are billions of magazines and books on this. I cannot name any off the top of my head because I never actually read them. LOL.).
If the misunderstandings are over nothing of importance, and can be easily forgotten or remedied by whatever you two do together or it simply does not bother either of you that much, then I doubt there is anything you should go out of your way to change the way you say things to accomodate. If, however, these misunderstandings are frequent and causing significant distress in your relationship, I recommend searching for as many resources you can on relationships and psychology, and possibly books on semantics/etiquette/diplomacy.
Good luck. Let me know if I have been unclear in any way.